Let's see, here's my list of the top 18 missing civilizations in CVI:
1. Persia
2. Mongolia
3. Assyria
4. Babylon
5. Inca
6. Maya
7. Byzantium
8. Ottomans/Turkey
9. Ethiopia
10. Hittite
11. Carthage
12. Korea
13. Siam
14. Moors (or Morocco)
15. Netherlands
16. Portugal
17. Holy Roman Empire
18. Mali
Besides those;, Italy, Austria, Poland, Prussia, Hungary, Iroquois, Cherokee, Israel, Ashanti, Zulu, Phoenicia, Tibet, Khmer, Vietnam, Macedonia, Minoans, Celts, Goths(Visigoths), Slavs(Wends), Sweden, Denmark, Scotland, Kush(or Nubia), Armenia(ancient kingdom), Parthia, Gaul...
There are several more choices, civilizations or fascinating tribes.
As long as relevant historically (for a period of more than a handful of years) and offering interesting Great Leader and (especially) Uniques, should be considered.
I'd like to add USSR to this list, fascinating, unique and original, so what if Russian speaking like Russia, Americans speak English in the game just like the English do (only with a different accent).
Forgot to add Canada and Australia up there as well!
Why not? Brazil's in.